Something that's missing from a lot of suggestions: Except for Quatermain, the LoeG was essentially drawn from villians and monsters, not heroes.
Nemo was an antihero.
Griffin (the invisible man) was a straight-up villian.
Hyde was a monster.
Mina wasn't a monster or villian, but nor was she a hero: she was a victim.
The only hero was Quatermain, and at the beginning of the comic, he's lost himself to opium.
The problem you'd have with that, though, is that Victorian Literature is full of monsters, while we tend to focus more on the heroes.
My picks:
Dana Scully (X-Files)
Hannibal Lector (Red Dragon, et al.)
Selina Kyle (Batman)
T-800 (The Terminator, et al.)
Robert Muldoon (Jurassic Park)
Dana Scully fits nicely into Mina's Shoes as team leader. She has a lot of experience dealing with weirdness, and a lot of experience keeping zany teammates in line. I also imagine her with a bit of alien technology, helping to beef up the team in the gear department.
Hannibal Lector is the best (and worst) planner that the team could possibly have. And he ties back into the "team of villians" thing.
T-800 provides a better beatdown than Hyde ever could. And he's programmed to follow Scully's every order.
Muldoon wasn't a particularly important character in Jurassic Park, but he was probably the most capable one. Plus, he's got a good grasp on technology--His job at Jurassic Park and his previous experiences gave him experience with a variety of weaponry and vehicles.
Catwoman is an iconic anti-hero and an iconic sneak. Plus, she's a top of the line unarmed combatant--if she can hold her own against batman, I can't think of many folks who could stand up to her.